The National League club say never-seen-before levels of injuries mean they need to play a young team at Bedford Town.
They drew 3-3 with the Southern League side on Saturday and could only name two substitutes.
Shots explained their stance in a statement and they hope fans will still travel and get behind the inexperienced side.
It read: “Due to the insurmountable amount of injuries we have sustained to our first team squad we will be sending a squad made of Academy players to tomorrow night’s replay against Bedford Town.
“Due to FA rules we could not add to our first team squad in time for tomorrow night’s replay as players must be registered to the club the day before the original tie and we could also not postpone the fixture to a later date as competition rules require the replay to be played by Thursday night at the latest despite our best efforts to have the tie played before the 2nd Round tie at Chesterfield was due to take place.
“At this moment in time we only have 10 fit first team players available for selection and have the prospect of four games in 10 days over the Christmas period. This wasn’t a decision that was made lightly, but we felt we couldn’t risk losing additional players in fixtures that are above and beyond our league schedule and not be able to have a squad to fulfil our league games over this busy period.
“We felt we had to make supporters aware of this situation and incredibly difficult decision we’ve had to make in advance of travelling to Bedford.
“Tuesday night’s replay is still an official first team fixture and we encourage supporters to get down to Bedford and support the young lads!”